kemalandClaude Opus 5.5
58dbd8f514
- DB build resolves the PGX-007 tag variants from the manifest's probes; coverage over all gene kinds. - Variant-based genes reported per variant (rs.. REF/ALT | Reference) with the CPIC lowest-activity diplotype; tagging genes as positive/negative with the population caveat; GSTM1/GSTT1/UGT2B17 *0 from targeted CN. - Case-insensitive phenotype keys (MT-RNR1). GeT-RM check extended to VKORC1 and the CN genes: 131/144 gene calls (docs/validation/V2_pgx_star.md). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
288 lines
4.8 KiB
JSON
288 lines
4.8 KiB
JSON
{
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"individuals": 30,
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"genes": {
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"CYP2B6": {
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"n": 14,
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"top": 12,
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"equivalent": 12,
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"not_comparable": 1
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},
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"CYP2C19": {
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"n": 15,
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"top": 14,
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"equivalent": 15
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},
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"CYP2C9": {
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"n": 15,
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"top": 15,
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"equivalent": 15
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},
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"CYP2D6": {
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"n": 15,
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"top": 12,
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"equivalent": 14
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},
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"CYP3A5": {
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"n": 15,
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"top": 15,
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"equivalent": 15
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},
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"CYP4F2": {
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"n": 9,
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"top": 8,
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"equivalent": 8
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},
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"GSTM1": {
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"n": 9,
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"top": 9,
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"equivalent": 9
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},
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"GSTT1": {
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"n": 9,
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"top": 7,
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"equivalent": 7
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},
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"NAT2": {
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"n": 9,
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"top": 8,
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"equivalent": 8
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},
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"NUDT15": {
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"n": 1,
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"top": 1,
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"equivalent": 1
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},
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"SLCO1B1": {
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"n": 15,
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"top": 9,
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"equivalent": 9
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},
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"TPMT": {
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"n": 16,
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"top": 15,
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"equivalent": 15
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},
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"UGT1A1": {
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"n": 9,
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"top": 0,
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"equivalent": 1
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},
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"UGT2B17": {
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"n": 2,
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"top": 2,
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"equivalent": 2
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},
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"VKORC1": {
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"n": 15,
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"equivalent": 13
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}
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},
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"legacy_nomenclature_genes": [
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"SLCO1B1",
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"UGT1A1"
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],
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"total": {
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"n": 144,
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"top": 131,
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"equivalent": 134
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},
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"discordant": [
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{
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"individual": "NA12156",
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"gene": "CYP4F2",
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"truth": "(*2)/*3",
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"call": "*1/*3",
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{
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{
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"truth": "*60/*28",
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"within_equivalents": false
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{
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"individual": "NA12044",
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{
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{
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"individual": "NA06991",
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{
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"individual": "NA06991",
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"gene": "VKORC1",
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"truth": "AA",
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"call": "rs9923231 T/T",
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"within_equivalents": false
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{
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"individual": "NA12878",
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"gene": "CYP2D6",
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"truth": "*3/(*68)+*4",
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"call": "*4x2/*1;*4x2/*82",
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"within_equivalents": false
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{
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"individual": "NA12878",
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},
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{
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"individual": "NA11993",
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{
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"individual": "NA11993",
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"call": "*28/*80",
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"within_equivalents": false
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{
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"individual": "NA12003",
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"gene": "UGT1A1",
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"truth": "*60/*28",
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"call": "*28/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA12003",
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"gene": "VKORC1",
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"truth": "AA",
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"call": "rs9923231 T/T",
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"within_equivalents": false
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},
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{
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"individual": "NA12003",
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"gene": "GSTT1",
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"truth": "(*A/*A)",
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"call": "*1/*0",
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"within_equivalents": false
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},
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{
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"individual": "NA07029",
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"gene": "CYP2B6",
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"truth": "*6/(*27)",
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{
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"individual": "NA07029",
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"gene": "CYP2C19",
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"truth": "*8/*17",
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"call": "*1/*17",
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"within_equivalents": true
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{
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"individual": "NA07029",
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"gene": "UGT1A1",
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"truth": "*1/*1",
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"call": "*1/*28",
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"within_equivalents": true
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{
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"individual": "NA12892",
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"gene": "CYP2B6",
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"truth": "*1/*1",
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"call": "*1/*5",
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"within_equivalents": false
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{
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"individual": "NA11832",
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"gene": "NAT2",
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"truth": "*5/(*12)",
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"call": "*1/*5",
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"within_equivalents": false
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},
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{
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"individual": "NA11832",
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"gene": "SLCO1B1",
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"truth": "*1/*1",
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"call": "*14/*20",
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"within_equivalents": false
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},
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{
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"individual": "NA11832",
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"gene": "UGT1A1",
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"truth": "(*28 + *60)/*60",
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"call": "*28/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA10838",
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"gene": "CYP2D6",
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"truth": "*2/*4",
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"call": "*1/*4;*2/*4",
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"within_equivalents": true
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},
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{
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"individual": "NA10838",
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"gene": "SLCO1B1",
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"truth": "*1/*1",
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"call": "*1/*14",
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"within_equivalents": false
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{
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"individual": "NA12813",
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"gene": "CYP2D6",
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"truth": "*2/*4",
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"call": "*1/*4;*2/*4",
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"within_equivalents": true
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},
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{
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"individual": "NA12813",
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"gene": "SLCO1B1",
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"truth": "*1/*21",
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"call": "*1/*20",
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"within_equivalents": false
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},
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{
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"individual": "NA12813",
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"gene": "UGT1A1",
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"truth": "(*28 + *60)/(*28 + *60)",
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"call": "*80/*80",
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"within_equivalents": false
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},
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{
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"individual": "NA12813",
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"gene": "GSTT1",
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"truth": "(*A/*A)",
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"call": "*1/*0",
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"within_equivalents": false
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},
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{
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"individual": "NA11881",
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"gene": "SLCO1B1",
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"truth": "*1/(*15)",
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"call": "*14/*15",
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"within_equivalents": false
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}
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]
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} |